Yes, it is possible due to many different reasons from hybridization to wrong taxonomy. Also, 16S RNA evolves very slowly and can be the same in closely related species.

Thank you for mentioning hybridization, Sir Andrey Yurchenko. But does that mean it is not advisable to use 16S rRNA for haplotype variation? 

Yes, it is not the best choice for the closely related species. CO1 or D-loop are much more suitable for invertebrates. 

Hi Sir, thank you. My adviser is still not successful in amplifying and sequencing the CO1 region; however, the protocol works great for 16S. I also don't have the luxury of time at this point. I still have observed variations using 16S. Any comments for 12S?

Thank you Sir. 

The same story for 12S, it is a very conservative region. 

Hello Sir Andrey Yurchenko, 

If you have the time, I wish you could reply.

First, I have samples from different populations and locations, but they have the same haplotype. This highly suggests that all samples belong to one species, right? 

Second, I've read on interspecific hybrids. Since you've also mentioned this before, would you kindly share your insights, how is hybridization related to the presence of different species sharing one haplotype (or same species with different haplotypes)?

These are only based on 16S region.

Thank you very much, Sir.

I would suggest that you keep in mind that in the big picture you are sampling a tiny fraction of the genome and trying to base a taxonomic decision on this single character, in this case a fragment of the 16S gene. We know that different genes, and different noncoding sequences, in different regions of the genome have vastly differing functions and differ by orders of magnitude in the rate at which mutations occur, as well as an enormous diversity in the manner and frequency in which mutations accumulate in different parts of the genome, i.e. think about inversions versus translocations versus point mutations (indels/substitutions). So, picking the appropriate gene in terms of mutation rate, should match the hypothetical timing these lineages shared a MRCA is important. In otehr words are we estimating lineage bifurcation for closely related species at a scale of 1 millions or 2 yrs, 10 millions years, 25, 50 myrs? This is important because for rRNA genes whether nuclear or mtDNA, substitution rates are relatively slow, so for divergences that less than 35 myrs you may not see any differences, even though the lineages are separate species. You can have morphological / behavioral differences between 2 species from different sample localities that share a single haplotype if the species diverged recently, say within a few thousand years, because the gene you are using evolves more slowly than morphology and behavior, which under strong natural selection can diverge in only a small number of generations. This is known as incomplete lineage sorting, in order to determine whether this is a soft polytomy, additional loci such as more rapidly evolving regions such as the widely used COI gene should be added to the data set. If logistically this is not feasible, you could propose that these are two closely related species, possibly undergoing insipient rapid speciation, but also acknowledge possibilities of incomplete lineage sorting, and hybridization. Additional life history data can also inform which mechanism is most likely operating, for example depending on reproductive strategy and dispersal ability. Either way this is still an interesting result, you can make it more interesting by summarizing all of the non genetic data that supports the existence of two lineages, and propose future efforts to include more rapidly evolving loci such as nuclear microsatellites, SNPs, EF1alpha, COI, COII, COIII ND4 etc.